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## M

m - Variable in class org.metaqtl.MultiFitResult
  The number of parameters
m1 - Variable in class org.metaqtl.Qtl
  The indice of the left flanking marker.
m2 - Variable in class org.metaqtl.Qtl
  The indice of the right flanking marker.
main(String[]) - Static method in class org.metaqtl.main.A2Xml
main(String[]) - Static method in class org.metaqtl.main.ConsMap
main(String[]) - Static method in class org.metaqtl.main.InfoMap
main(String[]) - Static method in class org.metaqtl.main.MapView
main(String[]) - Static method in class org.metaqtl.main.MetaDB
main(String[]) - Static method in class org.metaqtl.main.MMapView
main(String[]) - Static method in class org.metaqtl.main.MQTLView
main(String[]) - Static method in class org.metaqtl.main.QTLClust
main(String[]) - Static method in class org.metaqtl.main.QTLClustInfo
main(String[]) - Static method in class org.metaqtl.main.QTLModel
main(String[]) - Static method in class org.metaqtl.main.QTLProj
main(String[]) - Static method in class org.metaqtl.main.QTLTree
main(String[]) - Static method in class org.metaqtl.main.Xml2A
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaCMS
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaDraw
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaMapDraw
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaSimu
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
MAKER_NAME_VSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
manageMissingData(int) - Method in class org.metaqtl.MetaQtlData
  Manage the missing data.
MapChartFactory - Class in org.thalia.bio.entity.factory
  General comments must be added here.
MapChartFactory() - Constructor for class org.thalia.bio.entity.factory.MapChartFactory
MapCluster - Class in org.metaqtl
MapCluster() - Constructor for class org.metaqtl.MapCluster
  Creates a new instance of `MapCluster`.
MapDBFactory - Class in org.metaqtl.factory
  A factory to read the list and the properties of a set of genetic maps.
MapDBFactory() - Constructor for class org.metaqtl.factory.MapDBFactory
MapMakerFactory - Class in org.thalia.bio.entity.factory
MapMakerFactory() - Constructor for class org.thalia.bio.entity.factory.MapMakerFactory
mapName - Variable in class org.metaqtl.Chromosome
  The name of the map in which this chromosome is defined.
mapNames - Variable in class org.metaqtl.MetaChrom
  The names of the genetic maps.
mapOrigin - Variable in class org.metaqtl.Qtl.QTLProj
  The name of the map from which this QTL comes.
MAPPING_CROSS - Static variable in interface org.metaqtl.IBioGenomeProperties
  The key for mapping cross.
MAPPING_EXPANSION - Static variable in interface org.metaqtl.IBioGenomeProperties
  The key for mapping expansion status.
MAPPING_FUNCTION - Static variable in interface org.metaqtl.IBioGenomeProperties
  The key for mapping function.
MAPPING_FUNCTION_HALDANE - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for Haldane mapping function.
MAPPING_FUNCTION_HALDANE - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for haldane mapping function
MAPPING_FUNCTION_KOSAMBI - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for Kosambi mapping function.
MAPPING_FUNCTION_KOSAMBI - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for kosambi mapping function
MAPPING_FUNCTION_UNKNOWN - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for not defined mapping function
MAPPING_UNIT - Static variable in interface org.metaqtl.IBioGenomeProperties
  The mapping unit key.
MAPPING_UNIT_CM - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for centi-Morgan unit.
MAPPING_UNIT_CM - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for centi morgan mapping unit
MAPPING_UNIT_M - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for Morgan unit.
MAPPING_UNIT_M - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for morgan mapping unit
MAPPING_UNIT_UNKNOWN - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for unknown mapping unit
MappingFunction - Class in org.metaqtl.util
  define all cartogarphies functions
MappingFunction() - Constructor for class org.metaqtl.util.MappingFunction
MapRawFactory - Class in org.thalia.bio.entity.factory
MapRawFactory() - Constructor for class org.thalia.bio.entity.factory.MapRawFactory
mapScale - Variable in class org.metaqtl.Qtl.QTLProj
  The scale ratio between the original map and the map on which the QTL has been projected.
MapTabFactory - Class in org.thalia.bio.entity.factory
MapTabFactory() - Constructor for class org.thalia.bio.entity.factory.MapTabFactory
MapView - Class in org.metaqtl.main
MapView() - Constructor for class org.metaqtl.main.MapView
mapWeight - Variable in class org.metaqtl.Qtl.QTLProj
  The cumulated scale weights of the common marke sequences between the original map and the map on which the QTL has been projected.
Marker - Class in org.thalia.bio.entity
  Class Description Here
Marker() - Constructor for class org.thalia.bio.entity.Marker
Marker(String, IBioEntity) - Constructor for class org.thalia.bio.entity.Marker
MARKER - Static variable in interface org.thalia.bio.IBioLocus
MARKER_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
MARKER_POSITION_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
MARKERLOCUS - Static variable in interface org.thalia.bio.IBioEntityTypes
mcidx - Variable in class org.metaqtl.CMarkerSequence
  The common marker indices on the chromosomes.
merge(GeneticMap) - Method in class org.thalia.bio.entity.GeneticMap
  Deprecated.
mergeGenome(IBioGenome, IBioGenome) - Static method in class org.thalia.bio.util.BioUtilities
  This method merges two genomes in a single one : `g1` is modified and will contain the result of the merge.
MetaAlgorithm - Class in org.metaqtl.algo
MetaAlgorithm() - Constructor for class org.metaqtl.algo.MetaAlgorithm
MetaChrom - Class in org.metaqtl
  A MetaChrom is the result of the merge of the members of a `ChromCluster`.
MetaChrom(MultiFitResult, ChromCluster) - Constructor for class org.metaqtl.MetaChrom
  Get a new instance of `MetaChrom` which is initialized by using the result of the merge of the members of a `ChromCluster`.
MetaCMS - Class in org.thalia.metaqtl.main
MetaCMS() - Constructor for class org.thalia.metaqtl.main.MetaCMS
MetaDB - Class in org.metaqtl.main
MetaDB() - Constructor for class org.metaqtl.main.MetaDB
MetaDico - Class in org.metaqtl
  This class represents a dictionnary of synonyms.
MetaDico() - Constructor for class org.metaqtl.MetaDico
MetaDicoFactory - Class in org.metaqtl.factory
MetaDicoFactory() - Constructor for class org.metaqtl.factory.MetaDicoFactory
MetaDraw - Class in org.thalia.metaqtl.main
MetaDraw() - Constructor for class org.thalia.metaqtl.main.MetaDraw
MetaGraph - Class in org.metaqtl.graph
MetaGraph() - Constructor for class org.metaqtl.graph.MetaGraph
MetaGraphPar - Class in org.metaqtl.graph
MetaGraphParFactory - Class in org.metaqtl.factory
MetaGraphParFactory() - Constructor for class org.metaqtl.factory.MetaGraphParFactory
MetaMain - Class in org.metaqtl.main
MetaMain() - Constructor for class org.metaqtl.main.MetaMain
MetaMap - Class in org.metaqtl
  A `MetaMap` is a bundle of `MetaChrom` objects.
MetaMap(int) - Constructor for class org.metaqtl.MetaMap
  Creates a new instance of `MetaMap` which will contain `nchr` `MetaChrom` objects.
MetaMapAdapter - Class in org.metaqtl.adapter
  This class defines some usefull methods to adapt `MetaMap` objects into other kinds of objects or the inverse.
MetaMapAdapter() - Constructor for class org.metaqtl.adapter.MetaMapAdapter
MetaMapAlgorithm - Class in org.metaqtl.algo
  This class is dedicated to the construction of a consensus genetic map from a set of genetic maps based on a Weigthed Least Square approach.
MetaMapAlgorithm(IBioGenome[], IBioGenome, IBioLocus[], MetaDico) - Constructor for class org.metaqtl.algo.MetaMapAlgorithm
MetaMapDraw - Class in org.thalia.metaqtl.main
MetaMapDraw() - Constructor for class org.thalia.metaqtl.main.MetaMapDraw
MetaMapSummaryFactory - Class in org.metaqtl.factory
  A factory to write out the information on a `MetaMap`.
MetaMapSummaryFactory() - Constructor for class org.metaqtl.factory.MetaMapSummaryFactory
metaQtlAnalysis - Variable in class org.metaqtl.Chromosome
  The results of a meta-analysis of QTL.
MetaQtlAnalysis - Class in org.metaqtl
  A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlAnalysis(int) - Constructor for class org.metaqtl.MetaQtlAnalysis
  Creates a new instance of a `MetaQtlAnalysis`
MetaQtlAnalysisAdapter - Class in org.metaqtl.adapter
MetaQtlAnalysisAdapter() - Constructor for class org.metaqtl.adapter.MetaQtlAnalysisAdapter
MetaQtlAnalysisFactory - Class in org.metaqtl.factory
  A factory to deal with the result of a QTL meta-analysis.
MetaQtlAnalysisFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisFactory
MetaQtlAnalysisModelFactory - Class in org.metaqtl.factory
MetaQtlAnalysisModelFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisModelFactory
MetaQtlAnalysisSummaryFactory - Class in org.metaqtl.factory
  A factory to deal with QTL meta-analysis result.
MetaQtlAnalysisSummaryFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
MetaQtlData - Class in org.metaqtl
  QTL meta analysis first requires to gather the QTL according to the group trait they belong and then to format the QTL data into data points to perfom clustering.
MetaQtlData(Qtl[]) - Constructor for class org.metaqtl.MetaQtlData
  Create a new instance of `MetaQtlData` which will represent the given array of `Qtl`.
MetaQtlModel - Class in org.metaqtl
MetaQtlModel() - Constructor for class org.metaqtl.MetaQtlModel
MetaQtlModel(int) - Constructor for class org.metaqtl.MetaQtlModel
MetaQtlModelFactory - Class in org.metaqtl.factory
MetaQtlModelFactory() - Constructor for class org.metaqtl.factory.MetaQtlModelFactory
MetaQtlResult - Class in org.metaqtl
  A `MetaQtlResult` is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.
MetaQtlResult() - Constructor for class org.metaqtl.MetaQtlResult
MetaQtlResult(String, int) - Constructor for class org.metaqtl.MetaQtlResult
MetaSimu - Class in org.thalia.metaqtl.main
MetaSimu() - Constructor for class org.thalia.metaqtl.main.MetaSimu
MetaSimuStat - Class in org.thalia.metaqtl.main
MetaSimuStat() - Constructor for class org.thalia.metaqtl.main.MetaSimuStat
METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm
  A global variable to control the custering method.
mfc - Variable in class org.metaqtl.Chromosome
  The mapping function for this chromosome
mir - Variable in class org.metaqtl.EMCriteria
MMapView - Class in org.metaqtl.main
MMapView() - Constructor for class org.metaqtl.main.MMapView
mode - Variable in class org.metaqtl.QtlPartition
  The mode of representation
models - Variable in class org.metaqtl.MetaQtlModel
  The number of Qtl per chromosome and per trait.
mqtls - Variable in class org.metaqtl.Chromosome
  The meta Qtls on this chromosome.
MQTLView - Class in org.metaqtl.main
MQTLView() - Constructor for class org.metaqtl.main.MQTLView
mr - Variable in class org.metaqtl.Chromosome
  The adjacent recombination rate between ordered markers
mrkNames - Variable in class org.metaqtl.Chromosome
  The ordered marker names
mrkNames - Variable in class org.metaqtl.MetaChrom
  The ordered marker names.
mrkOc - Variable in class org.metaqtl.MetaChrom
  The number of occurence per marker oved chromosomes.
mStep(double[], double[], EMResult, double) - Static method in class org.metaqtl.algo.EMAlgorithm
  The Maximization step : here this step is straighforward and simple analytical formula are applied to obtain the new parameter estimates.
mu - Variable in class org.metaqtl.EMResult
  The means of the clusters.
MultiFitResult - Class in org.metaqtl
  This class represents a result of a multilinear regression analysis.
MultiFitResult(int, int) - Constructor for class org.metaqtl.MultiFitResult
  Creates a new instance of `MultiFitResult` with the given number of observations `N` and parameters `M`.
mut - Variable in class org.metaqtl.Chromosome
  The mapping unit for this chromosome

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